/tools/fastx_toolkit/fastx_reverse_complement.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 63 lines · 45 code · 16 blank · 2 comment · 0 complexity · 0b07d0930a4277fcb7d2d5805feaae6d MD5 · raw file
- <tool id="cshl_fastx_reverse_complement" name="Reverse-Complement">
- <description></description>
- <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
- <command>zcat -f '$input' | fastx_reverse_complement -v -o $output
- #if $input.ext == "fastqsanger":
- -Q 33
- #end if
- </command>
- <inputs>
- <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to reverse-complement" />
- </inputs>
- <tests>
- <test>
- <!-- Reverse-complement a FASTA file -->
- <param name="input" value="fastx_rev_comp1.fasta" />
- <output name="output" file="fastx_reverse_complement1.out" />
- </test>
- <test>
- <!-- Reverse-complement a FASTQ file -->
- <param name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/>
- <output name="output" file="fastx_reverse_complement2.out" />
- </test>
- </tests>
-
- <outputs>
- <data format="input" name="output" metadata_source="input" />
- </outputs>
- <help>
- **What it does**
- This tool reverse-complements each sequence in a library.
- If the library is a FASTQ, the quality-scores are also reversed.
-
- --------
- **Example**
- Input FASTQ file::
- @CSHL_1_FC42AGWWWXX:8:1:3:740
- TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA
- +CSHL_1_FC42AGWWWXX:8:1:3:740
- 33 33 33 34 33 33 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 27 21 27 33 32 31 29 26 24 5 5 15 17 27 26
- Output FASTQ file::
- @CSHL_1_FC42AGWWWXX:8:1:3:740
- TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA
- +CSHL_1_FC42AGWWWXX:8:1:3:740
- 26 27 17 15 5 5 24 26 29 31 32 33 27 21 27 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 33 33 34 33 33 33
- ------
- This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
- .. __: http://hannonlab.cshl.edu/fastx_toolkit/
-
- </help>
- </tool>